class MPDataRetrieval: """ MPDataRetrieval is used to retrieve data from the Materials Project database, print the results, and convert them into an indexed/unindexed Pandas dataframe. """ def __init__(self, api_key=None): """ Args: api_key: (str) Your Citrine API key, or None if you've set the CITRINE_KEY environment variable Returns: None """ self.mprester = MPRester(api_key=api_key) def get_dataframe(self, criteria, properties, mp_decode=False, index_mpid=True): """ Gets data from MP in a dataframe format. See API docs at https://materialsproject.org/wiki/index.php/The_Materials_API for more details. Args: criteria: (str/dict) Criteria of the query as a string or mongo-style dict. If string, it supports a powerful but simple string criteria. E.g., "Fe2O3" means search for materials with reduced_formula Fe2O3. Wild cards are also supported. E.g., "\*2O" means get all materials whose formula can be formed as \*2O, e.g., Li2O, K2O, etc. Other syntax examples: mp-1234: Interpreted as a Materials ID. Fe2O3 or \*2O3: Interpreted as reduced formulas. Li-Fe-O or \*-Fe-O: Interpreted as chemical systems. You can mix and match with spaces, which are interpreted as "OR". E.g. "mp-1234 FeO" means query for all compounds with reduced formula FeO or with materials_id mp-1234. Using a full dict syntax, even more powerful queries can be constructed. For example, {"elements":{"$in":["Li", "Na", "K"], "$all": ["O"]}, "nelements":2} selects all Li, Na and K oxides. {"band_gap": {"$gt": 1}} selects all materials with band gaps greater than 1 eV. properties: (list) Properties to request for as a list. For example, ["formula", "formation_energy_per_atom"] returns the formula and formation energy per atom. mp_decode: (bool) Whether to do a decoding to a Pymatgen object where possible. In some cases, it might be useful to just get the raw python dict, i.e., set to False. index_mpid: (bool) Whether to set the materials_id as the dataframe index. Returns: A Pandas dataframe object """ if index_mpid and "material_id" not in properties: properties.append("material_id") data = self.mprester.query(criteria, properties, mp_decode) df = pd.DataFrame(data, columns=properties) if index_mpid: df = df.set_index("material_id") return df
class MPResterTest(unittest.TestCase): def setUp(self): self.rester = MPRester() def test_get_data(self): props = ["energy", "energy_per_atom", "formation_energy_per_atom", "nsites", "unit_cell_formula", "pretty_formula", "is_hubbard", "elements", "nelements", "e_above_hull", "hubbards", "is_compatible", "task_ids", "density", "icsd_ids", "total_magnetization"] # unicode literals have been reintroduced in py>3.2 expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749, 28, {k: v for k, v in {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4}.items()}, "LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0, {k: v for k, v in {'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}.items()}, True, [u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820', u'mp-540081', u'mp-797269'], 3.4662026991351147, [159107, 154117, 160776, 99860, 181272, 166815, 260571, 92198, 165000, 155580, 38209, 161479, 153699, 260569, 260570, 200155, 260572, 181341, 181342, 72545, 56291, 97764, 162282, 155635], 16.0002716] for (i, prop) in enumerate(props): if prop not in ['hubbards', 'unit_cell_formula', 'elements', 'icsd_ids', 'task_ids']: val = self.rester.get_data("mp-19017", prop=prop)[0][prop] self.assertAlmostEqual(expected_vals[i], val) elif prop in ["elements", "icsd_ids", "task_ids"]: self.assertEqual(set(expected_vals[i]), set(self.rester.get_data("mp-19017", prop=prop)[0][prop])) else: self.assertEqual(expected_vals[i], self.rester.get_data("mp-19017", prop=prop)[0][prop]) props = ['structure', 'initial_structure', 'final_structure', 'entry'] for prop in props: print(prop) obj = self.rester.get_data("mp-19017", prop=prop)[0][prop] if prop.endswith("structure"): self.assertIsInstance(obj, Structure) elif prop == "entry": obj = self.rester.get_data("mp-19017", prop=prop)[0][prop] self.assertIsInstance(obj, ComputedEntry) #Test chemsys search data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula') self.assertTrue(len(data) > 1) elements = {Element("Li"), Element("Fe"), Element("O")} for d in data: self.assertTrue( set(Composition(d['unit_cell_formula']).elements).issubset( elements)) self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3", "badmethod") def test_get_materials_id_from_task_id(self): self.assertEqual(self.rester.get_materials_id_from_task_id( "mp-540081"), "mp-19017") def test_get_materials_id_references(self): # nosetests pymatgen/matproj/tests/test_rest.py:MPResterTest.test_get_materials_id_references m = MPRester() data = m.get_materials_id_references('mp-123') self.assertTrue(len(data) > 1000) def test_find_structure(self): # nosetests pymatgen/matproj/tests/test_rest.py:MPResterTest.test_find_structure m = MPRester() ciffile = os.path.join(test_dir, 'Fe3O4.cif') data = m.find_structure(ciffile) self.assertTrue(len(data) > 1) s = CifParser(ciffile).get_structures()[0] data = m.find_structure(s) self.assertTrue(len(data) > 1) def test_get_entries_in_chemsys(self): syms = ["Li", "Fe", "O"] entries = self.rester.get_entries_in_chemsys(syms) elements = set([Element(sym) for sym in syms]) for e in entries: self.assertIsInstance(e, ComputedEntry) self.assertTrue(set(e.composition.elements).issubset(elements)) def test_get_structure_by_material_id(self): s1 = self.rester.get_structure_by_material_id("mp-1") self.assertEqual(s1.formula, "Cs1") def test_get_entry_by_material_id(self): e = self.rester.get_entry_by_material_id("mp-19017") self.assertIsInstance(e, ComputedEntry) self.assertTrue(e.composition.reduced_formula, "LiFePO4") def test_query(self): criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}} props = ['pretty_formula', 'energy'] data = self.rester.query(criteria=criteria, properties=props) self.assertTrue(len(data) > 6) data = self.rester.query(criteria="*2O", properties=props) self.assertGreaterEqual(len(data), 52) self.assertIn("Li2O", (d["pretty_formula"] for d in data)) def test_get_exp_thermo_data(self): data = self.rester.get_exp_thermo_data("Fe2O3") self.assertTrue(len(data) > 0) for d in data: self.assertEqual(d.formula, "Fe2O3") def test_get_dos_by_id(self): dos = self.rester.get_dos_by_material_id("mp-2254") self.assertIsInstance(dos, CompleteDos) def test_get_bandstructure_by_material_id(self): bs = self.rester.get_bandstructure_by_material_id("mp-2254") self.assertIsInstance(bs, BandStructureSymmLine) def test_get_structures(self): structs = self.rester.get_structures("Mn3O4") self.assertTrue(len(structs) > 0) def test_get_entries(self): entries = self.rester.get_entries("TiO2") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.composition.reduced_formula, "TiO2") entries = self.rester.get_entries("TiO2", inc_structure="final") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.structure.composition.reduced_formula, "TiO2") all_entries = self.rester.get_entries("Fe", compatible_only=False) entries = self.rester.get_entries("Fe", compatible_only=True) self.assertTrue(len(entries) < len(all_entries)) entries = self.rester.get_entries("Fe", compatible_only=True, property_data=["cif"]) self.assertIn("cif", entries[0].data) def test_get_exp_entry(self): entry = self.rester.get_exp_entry("Fe2O3") self.assertEqual(entry.energy, -825.5) def test_submit_query_delete_snl(self): s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]]) # d = self.rester.submit_snl( # [s, s], remarks=["unittest"], # authors="Test User <*****@*****.**>") # self.assertEqual(len(d), 2) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 2) # snlids = [d["_id"] for d in data] # self.rester.delete_snl(snlids) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 0) def test_get_stability(self): entries = self.rester.get_entries_in_chemsys(["Fe", "O"]) modified_entries = [] for entry in entries: # Create modified entries with energies that are 0.01eV higher # than the corresponding entries. if entry.composition.reduced_formula == "Fe2O3": modified_entries.append( ComputedEntry(entry.composition, entry.uncorrected_energy + 0.01, parameters=entry.parameters, entry_id="mod_{}".format(entry.entry_id))) rest_ehulls = self.rester.get_stability(modified_entries) all_entries = entries + modified_entries compat = MaterialsProjectCompatibility() all_entries = compat.process_entries(all_entries) pd = PhaseDiagram(all_entries) a = PDAnalyzer(pd) for e in all_entries: if str(e.entry_id).startswith("mod"): for d in rest_ehulls: if d["entry_id"] == e.entry_id: data = d break self.assertAlmostEqual(a.get_e_above_hull(e), data["e_above_hull"]) def test_get_reaction(self): rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"]) self.assertIn("Li2O", rxn["Experimental_references"]) def test_get_substrates(self): substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0]) substrates = [sub_dict['sub_id'] for sub_dict in substrate_data] self.assertIn("mp-2534", substrates) def test_parse_criteria(self): crit = MPRester.parse_criteria("mp-1234 Li-*") self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"]) self.assertIn({"task_id": "mp-1234"}, crit["$or"]) crit = MPRester.parse_criteria("Li2*") self.assertIn("Li2O", crit["pretty_formula"]["$in"]) self.assertIn("Li2I", crit["pretty_formula"]["$in"]) self.assertIn("CsLi2", crit["pretty_formula"]["$in"]) crit = MPRester.parse_criteria("Li-*-*") self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"]) self.assertNotIn("Li-Li", crit["chemsys"]["$in"]) comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"] for c in comps: self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c) chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"] self.assertEqual(len(chemsys), 2) comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"] self.assertEqual(len(comps), 3, comps) #Let's test some invalid symbols self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe") self.assertRaises(ValueError, MPRester.parse_criteria, "LO2") crit = MPRester.parse_criteria("POPO2") self.assertIn("P2O3", crit["pretty_formula"]["$in"])
class MPResterTest(unittest.TestCase): def setUp(self): self.rester = MPRester() def test_get_data(self): props = [ "energy", "energy_per_atom", "formation_energy_per_atom", "nsites", "unit_cell_formula", "pretty_formula", "is_hubbard", "elements", "nelements", "e_above_hull", "hubbards", "is_compatible", "task_ids", "density", "icsd_ids", "total_magnetization" ] # unicode literals have been reintroduced in py>3.2 expected_vals = [ -191.33812137, -6.833504334642858, -2.551358929370749, 28, {k: v for k, v in { 'P': 4, 'Fe': 4, 'O': 16, 'Li': 4 }.items()}, "LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0, { k: v for k, v in { 'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0 }.items() }, True, [ u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820', u'mp-540081', u'mp-797269' ], 3.4662026991351147, [ 159107, 154117, 160776, 99860, 181272, 166815, 260571, 92198, 165000, 155580, 38209, 161479, 153699, 260569, 260570, 200155, 260572, 181341, 181342, 72545, 56291, 97764, 162282, 155635 ], 16.0002716 ] for (i, prop) in enumerate(props): if prop not in [ 'hubbards', 'unit_cell_formula', 'elements', 'icsd_ids', 'task_ids' ]: val = self.rester.get_data("mp-19017", prop=prop)[0][prop] self.assertAlmostEqual(expected_vals[i], val) elif prop in ["elements", "icsd_ids", "task_ids"]: self.assertEqual( set(expected_vals[i]), set(self.rester.get_data("mp-19017", prop=prop)[0][prop])) else: self.assertEqual( expected_vals[i], self.rester.get_data("mp-19017", prop=prop)[0][prop]) props = ['structure', 'initial_structure', 'final_structure', 'entry'] for prop in props: obj = self.rester.get_data("mp-19017", prop=prop)[0][prop] if prop.endswith("structure"): self.assertIsInstance(obj, Structure) elif prop == "entry": obj = self.rester.get_data("mp-19017", prop=prop)[0][prop] self.assertIsInstance(obj, ComputedEntry) #Test chemsys search data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula') self.assertTrue(len(data) > 1) elements = {Element("Li"), Element("Fe"), Element("O")} for d in data: self.assertTrue( set(Composition( d['unit_cell_formula']).elements).issubset(elements)) self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3", "badmethod") def test_get_materials_id_from_task_id(self): self.assertEqual( self.rester.get_materials_id_from_task_id("mp-540081"), "mp-19017") def test_get_materials_id_references(self): # nosetests pymatgen/matproj/tests/test_rest.py:MPResterTest.test_get_materials_id_references m = MPRester() data = m.get_materials_id_references('mp-123') self.assertTrue(len(data) > 1000) def test_find_structure(self): # nosetests pymatgen/matproj/tests/test_rest.py:MPResterTest.test_find_structure m = MPRester() ciffile = os.path.join(test_dir, 'Fe3O4.cif') data = m.find_structure(ciffile) self.assertTrue(len(data) > 1) s = CifParser(ciffile).get_structures()[0] data = m.find_structure(s) self.assertTrue(len(data) > 1) def test_get_entries_in_chemsys(self): syms = ["Li", "Fe", "O"] entries = self.rester.get_entries_in_chemsys(syms) elements = set([Element(sym) for sym in syms]) for e in entries: self.assertIsInstance(e, ComputedEntry) self.assertTrue(set(e.composition.elements).issubset(elements)) def test_get_structure_by_material_id(self): s1 = self.rester.get_structure_by_material_id("mp-1") self.assertEqual(s1.formula, "Cs1") def test_get_entry_by_material_id(self): e = self.rester.get_entry_by_material_id("mp-19017") self.assertIsInstance(e, ComputedEntry) self.assertTrue(e.composition.reduced_formula, "LiFePO4") def test_query(self): criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}} props = ['pretty_formula', 'energy'] data = self.rester.query(criteria=criteria, properties=props) self.assertTrue(len(data) > 6) data = self.rester.query(criteria="*2O", properties=props) self.assertGreaterEqual(len(data), 52) self.assertIn("Li2O", (d["pretty_formula"] for d in data)) def test_get_exp_thermo_data(self): data = self.rester.get_exp_thermo_data("Fe2O3") self.assertTrue(len(data) > 0) for d in data: self.assertEqual(d.formula, "Fe2O3") def test_get_dos_by_id(self): dos = self.rester.get_dos_by_material_id("mp-2254") self.assertIsInstance(dos, CompleteDos) def test_get_bandstructure_by_material_id(self): bs = self.rester.get_bandstructure_by_material_id("mp-2254") self.assertIsInstance(bs, BandStructureSymmLine) def test_get_structures(self): structs = self.rester.get_structures("Mn3O4") self.assertTrue(len(structs) > 0) def test_get_entries(self): entries = self.rester.get_entries("TiO2") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.composition.reduced_formula, "TiO2") entries = self.rester.get_entries("TiO2", inc_structure="final") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.structure.composition.reduced_formula, "TiO2") all_entries = self.rester.get_entries("Fe", compatible_only=False) entries = self.rester.get_entries("Fe", compatible_only=True) self.assertTrue(len(entries) < len(all_entries)) entries = self.rester.get_entries("Fe", compatible_only=True, property_data=["cif"]) self.assertIn("cif", entries[0].data) def test_get_exp_entry(self): entry = self.rester.get_exp_entry("Fe2O3") self.assertEqual(entry.energy, -825.5) def test_submit_query_delete_snl(self): s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]]) # d = self.rester.submit_snl( # [s, s], remarks=["unittest"], # authors="Test User <*****@*****.**>") # self.assertEqual(len(d), 2) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 2) # snlids = [d["_id"] for d in data] # self.rester.delete_snl(snlids) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 0) def test_get_stability(self): entries = self.rester.get_entries_in_chemsys(["Fe", "O"]) modified_entries = [] for entry in entries: # Create modified entries with energies that are 0.01eV higher # than the corresponding entries. if entry.composition.reduced_formula == "Fe2O3": modified_entries.append( ComputedEntry(entry.composition, entry.uncorrected_energy + 0.01, parameters=entry.parameters, entry_id="mod_{}".format(entry.entry_id))) rest_ehulls = self.rester.get_stability(modified_entries) all_entries = entries + modified_entries compat = MaterialsProjectCompatibility() all_entries = compat.process_entries(all_entries) pd = PhaseDiagram(all_entries) a = PDAnalyzer(pd) for e in all_entries: if str(e.entry_id).startswith("mod"): for d in rest_ehulls: if d["entry_id"] == e.entry_id: data = d break self.assertAlmostEqual(a.get_e_above_hull(e), data["e_above_hull"]) def test_get_reaction(self): rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"]) self.assertIn("Li2O", rxn["Experimental_references"]) def test_parse_criteria(self): crit = MPRester.parse_criteria("mp-1234 Li-*") self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"]) self.assertIn({"task_id": "mp-1234"}, crit["$or"]) crit = MPRester.parse_criteria("Li2*") self.assertIn("Li2O", crit["pretty_formula"]["$in"]) self.assertIn("Li2I", crit["pretty_formula"]["$in"]) self.assertIn("CsLi2", crit["pretty_formula"]["$in"]) crit = MPRester.parse_criteria("Li-*-*") self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"]) self.assertNotIn("Li-Li", crit["chemsys"]["$in"]) comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"] for c in comps: self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c) chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"] self.assertEqual(len(chemsys), 2) comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"] self.assertEqual(len(comps), 3, comps) #Let's test some invalid symbols self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe") self.assertRaises(ValueError, MPRester.parse_criteria, "LO2") crit = MPRester.parse_criteria("POPO2") self.assertIn("P2O3", crit["pretty_formula"]["$in"])
colnames = ['p-type', 'n-type'] df = pandas.read_csv('Best_n_p_TEs.csv', names=colnames) input_data_ptype = df['p-type'].tolist()[1:] y = 0 compositions = [] for column in df: if column == 'p-type': te_type = 'p-type' elif column == 'n-type': te_type = 'n-type' for compound in df[column].tolist()[1:]: if not pandas.isnull(compound) and Composition(compound) not in compositions: c = Composition(compound) compositions.append(c) center = get_band_center(c) comp_results = mpr.query(c.reduced_formula, properties=['band_gap', 'material_id', 'icsd_id', 'e_above_hull']) try: i = comp_results[0] min_e_above_hull = i['e_above_hull'] except: y += 1 print 'No compounds exists in MP for ' + c.reduced_formula continue for x in range(1, len(comp_results)): if comp_results[x]['e_above_hull'] < min_e_above_hull: i = comp_results[x] min_e_above_hull = comp_results[x]['e_above_hull'] print ','.join([str(x) for x in c.formula, c.reduced_formula, center + i['band_gap'] / 2, center, center, center - i[ 'band_gap'] / 2, i['material_id'], i['icsd_id'], column]) csv_outfile.writerow(
from pymatgen import Composition, Element from pymatgen.matproj.rest import MPRester __author__ = 'Anubhav Jain' __copyright__ = 'Copyright 2014, The Materials Project' __version__ = '0.1' __maintainer__ = 'Anubhav Jain' __email__ = '*****@*****.**' __date__ = 'Oct 01, 2014' def get_band_center(form): c = Composition(str(form)) prod = 1.0 for el, amt in c.get_el_amt_dict().iteritems(): prod = prod * (Element(el).X ** amt) return -prod ** (1 / sum(c.get_el_amt_dict().values())) if __name__ == '__main__': mpr = MPRester() for i in mpr.query({"elements": {"$in": ["O", "S", "Se", "Te"]}, "nelements": 2, "e_above_hull": {"$lte": 0.05}}, properties=['band_gap', 'formula', 'material_id', 'icsd_id']): c = Composition(i['formula']) center = get_band_center(c) print ','.join([str(x) for x in c.formula, c.reduced_formula, center, center + i['band_gap'] / 2, center - i['band_gap'] / 2, i[ 'material_id'], i['icsd_id']])
class MPResterTest(unittest.TestCase): def setUp(self): self.rester = MPRester() def test_get_data(self): props = ["energy", "energy_per_atom", "formation_energy_per_atom", "nsites", "unit_cell_formula", "pretty_formula", "is_hubbard", "elements", "nelements", "e_above_hull", "hubbards", "is_compatible", "task_ids", "density", "icsd_ids", "total_magnetization"] expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749, 28, {u'P': 4, u'Fe': 4, u'O': 16, u'Li': 4}, "LiFePO4", True, [u'Li', u'O', u'P', u'Fe'], 4, 0.0, {u'Fe': 5.3, u'Li': 0.0, u'O': 0.0, u'P': 0.0}, True, ['mp-540081', 'mp-601412', 'mp-19017'], 3.4662026991351147, [159107, 154117, 160776, 99860, 181272, 166815, 260571, 92198, 165000, 155580, 38209, 161479, 153699, 260569, 260570, 200155, 260572, 181341, 181342, 72545, 56291, 97764, 162282, 155635], 16.0002716] for (i, prop) in enumerate(props): if prop not in ['hubbards', 'unit_cell_formula', 'elements', 'icsd_ids', 'task_ids']: val = self.rester.get_data("mp-19017", prop=prop)[0][prop] self.assertAlmostEqual(expected_vals[i], val) elif prop in ["elements", "icsd_ids", "task_ids"]: self.assertEqual(set(expected_vals[i]), set(self.rester.get_data("mp-19017", prop=prop)[0][prop])) else: self.assertEqual(expected_vals[i], self.rester.get_data("mp-19017", prop=prop)[0][prop]) props = ['structure', 'initial_structure', 'final_structure', 'entry'] for prop in props: obj = self.rester.get_data("mp-19017", prop=prop)[0][prop] if prop.endswith("structure"): self.assertIsInstance(obj, Structure) elif prop == "entry": obj = self.rester.get_data("mp-19017", prop=prop)[0][prop] self.assertIsInstance(obj, ComputedEntry) #Test chemsys search data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula') self.assertTrue(len(data) > 1) elements = {Element("Li"), Element("Fe"), Element("O")} for d in data: self.assertTrue( set(Composition(d['unit_cell_formula']).elements).issubset( elements)) self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3", "badmethod") def test_get_materials_id_from_task_id(self): self.assertEqual(self.rester.get_materials_id_from_task_id( "mp-540081"), "mp-19017") def test_get_entries_in_chemsys(self): syms = ["Li", "Fe", "O"] all_entries = self.rester.get_entries_in_chemsys(syms, False) entries = self.rester.get_entries_in_chemsys(syms) self.assertTrue(len(entries) <= len(all_entries)) elements = set([Element(sym) for sym in syms]) for e in entries: self.assertIsInstance(e, ComputedEntry) self.assertTrue(set(e.composition.elements).issubset(elements)) def test_get_structure_by_material_id(self): s1 = self.rester.get_structure_by_material_id("mp-1") self.assertEqual(s1.formula, "Cs1") def test_get_entry_by_material_id(self): e = self.rester.get_entry_by_material_id("mp-19017") self.assertIsInstance(e, ComputedEntry) self.assertTrue(e.composition.reduced_formula, "LiFePO4") def test_query(self): criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}} props = ['formula', 'energy'] data = self.rester.query(criteria=criteria, properties=props) self.assertTrue(len(data) > 6) def test_get_exp_thermo_data(self): data = self.rester.get_exp_thermo_data("Fe2O3") self.assertTrue(len(data) > 0) for d in data: self.assertEqual(d.formula, "Fe2O3") def test_get_dos_by_id(self): dos = self.rester.get_dos_by_material_id("mp-2254") self.assertIsInstance(dos, CompleteDos) def test_get_bandstructure_by_material_id(self): bs = self.rester.get_bandstructure_by_material_id("mp-2254") self.assertIsInstance(bs, BandStructureSymmLine) def test_get_structures(self): structs = self.rester.get_structures("Mn3O4") self.assertTrue(len(structs) > 0) def test_get_entries(self): entries = self.rester.get_entries("TiO2") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.composition.reduced_formula, "TiO2") entries = self.rester.get_entries("TiO2", inc_structure="final") self.assertTrue(len(entries) > 1) for e in entries: self.assertEqual(e.structure.composition.reduced_formula, "TiO2") def test_get_exp_entry(self): entry = self.rester.get_exp_entry("Fe2O3") self.assertEqual(entry.energy, -825.5) def test_submit_query_delete_snl(self): s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]]) # d = self.rester.submit_snl( # [s, s], remarks=["unittest"], # authors="Test User <*****@*****.**>") # self.assertEqual(len(d), 2) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 2) # snlids = [d["_id"] for d in data] # self.rester.delete_snl(snlids) # data = self.rester.query_snl({"about.remarks": "unittest"}) # self.assertEqual(len(data), 0) def test_get_stability(self): entries = self.rester.get_entries("Fe-O") modified_entries = [] for entry in entries: # Create modified entries with energies that are 0.01eV higher # than the corresponding entries. if entry.composition.reduced_formula == "Fe2O3": modified_entries.append( ComputedEntry(entry.composition, entry.uncorrected_energy + 0.01, parameters=entry.parameters, entry_id="mod_{}".format(entry.entry_id))) rest_ehulls = self.rester.get_stability(modified_entries) all_entries = entries + modified_entries compat = MaterialsProjectCompatibility() all_entries = compat.process_entries(all_entries) pd = PhaseDiagram(all_entries) a = PDAnalyzer(pd) for e in all_entries: if str(e.entry_id).startswith("mod"): for d in rest_ehulls: if d["entry_id"] == e.entry_id: data = d break self.assertAlmostEqual(a.get_e_above_hull(e), data["e_above_hull"]) def test_get_reaction(self): rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"]) self.assertIn("Li2O", rxn["Experimental_references"])
class MPDataRetrieval: """ MPDataRetrieval is used to retrieve data from the Materials Project database, print the results, and convert them into an indexed/unindexed Pandas dataframe. """ def __init__(self, api_key=None): """ Args: api_key: (str) Your Citrine API key, or None if you've set the MAPI_KEY environment variable Returns: None """ api_key = api_key if api_key else os.environ["MAPI_KEY"] self.mprester = MPRester(api_key=api_key) def get_dataframe(self, criteria, properties, mp_decode=False, index_mpid=True): """ Gets data from MP in a dataframe format. See API docs at https://materialsproject.org/wiki/index.php/The_Materials_API for more details. Args: criteria: (str/dict) Criteria of the query as a string or mongo-style dict. If string, it supports a powerful but simple string criteria. E.g., "Fe2O3" means search for materials with reduced_formula Fe2O3. Wild cards are also supported. E.g., "\*2O" means get all materials whose formula can be formed as \*2O, e.g., Li2O, K2O, etc. Other syntax examples: mp-1234: Interpreted as a Materials ID. Fe2O3 or \*2O3: Interpreted as reduced formulas. Li-Fe-O or \*-Fe-O: Interpreted as chemical systems. You can mix and match with spaces, which are interpreted as "OR". E.g. "mp-1234 FeO" means query for all compounds with reduced formula FeO or with materials_id mp-1234. Using a full dict syntax, even more powerful queries can be constructed. For example, {"elements":{"$in":["Li", "Na", "K"], "$all": ["O"]}, "nelements":2} selects all Li, Na and K oxides. {"band_gap": {"$gt": 1}} selects all materials with band gaps greater than 1 eV. properties: (list) Properties to request for as a list. For example, ["formula", "formation_energy_per_atom"] returns the formula and formation energy per atom. mp_decode: (bool) Whether to do a decoding to a Pymatgen object where possible. In some cases, it might be useful to just get the raw python dict, i.e., set to False. index_mpid: (bool) Whether to set the materials_id as the dataframe index. Returns: A Pandas dataframe object """ if index_mpid and "material_id" not in properties: properties.append("material_id") data = self.mprester.query(criteria, properties, mp_decode) df = pd.DataFrame(data, columns=properties) if index_mpid: df = df.set_index("material_id") return df